Freesurfer April 2007

freesurfer@nmr.mgh.harvard.edu

57 participants
78 discussions

credits for talk
by Kirk, Gregory 06 Apr '07

06 Apr '07

Hi Folks, I remember somewhere there was a page describing how we should put the credits for a publication. How do you want the credit to read for a clinical conference talk reporting freesurfer cortical thickness group study results G.

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patches from labels
by Don.Rojas＠UCHSC.edu 06 Apr '07

06 Apr '07

To all, I'm interested in creating some flattened patches from a region of auditory cortex. I have done the full recon-all processing on the datasets with version 3.0.4. Is there some way to create patch files without manually tracing the region you want to flatten in tksurfer? Is there a way to create patch files by combining several contiguous anatomical labels from the annotation file into one patch for flattening using mris_flatten? Thanks, Don Rojas University of Colorado

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Re: [Freesurfer] Recommended Linux flavour
by Istvan Akos Morocz 06 Apr '07

06 Apr '07

freesurfer works fine on Slackware too, v11.0 and v10.1, using Xeon chips. bye, pisti > Date: Thu, 05 Apr 2007 13:08:46 -0400 > From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Recommended Linux flavour > To: wade(a)ski.org > Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <1175792926.23596.9.camel(a)minerva.nmr.mgh.harvard.edu> > Content-Type: text/plain > > Alex, > > We use Centos 4 (both 32 and 64 bit) at the NMR Center, so freesurfer > works best with it (in that most problems are easy to fix since we can > recreate them easily). Others on the list has been successful with > Debian, SuSE, Ubuntu, Fedora Core and others. But there have been some > display issues with tksurfer with some of the very newest Linux > releases, like Fedora Core 6. > > Nick > > On Thu, 2007-04-05 at 09:39 -0700, Alex Wade wrote: >> We are about to install a few Linux workstations, primarily to run >> Freesurfer and MNISuite. Can I check on what the best Linux flavour >> is? Do you still recommend CentOS 4? >> thanks >> >> Alex >> >> >> >> -- >> A.R. Wade Ph.D. >> Associate Scientist >> The Smith-Kettlewell Eye Research Institute >> 2318 Fillmore Street >> San Francisco, CA 94115 >> >> tel. 415 345 2083 >> fax. 309 416 6533 >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ----- pisti(a)bwh.harvard.edu

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viewing group analysis results
by Chacko Cherian 06 Apr '07

06 Apr '07

Hello users, I am doing the group analysis stats results...using FDR correction 0.01 and checking the pial surface with curvature and overlay. I see this line come up whenever i change the FDR..is this some kind of error which I need to be concerned about? surfer: Error sending tcl command OverlayLayerChanged: bad window path name ".fsgdf-0" Thanks in advance. Regards Chacko. ____________________________________________________________________________________ Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo! Travel to find your fit. http://farechase.yahoo.com/promo-generic-14795097

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Re: Freesurfer and R
by Alessandro Gagliardi 05 Apr '07

05 Apr '07

I ended up trying a bit of a hack, and it seems to have worked, but I don't know if I can trust it. I used the AnalyzeFMRI package in R to output my data in an Analyze file. I had to change the voxel size and origin in the header manually. And then I copied a .mat file from another 3D Analyze file produced by FreeSurfer with the same dimensions as my output and named it the same as my new Analyze file. I don't really know how the .mat file works, so as I said, I don't know if I can trust it. The .mat file is from a the same data that I'm analyze in R, so it should have the same orientation. Perhaps one of the FreeSurfer gurus can tell me if this is a really stupid thing to do or not. Regards, -Alessandro On 4/4/07, freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Date: Wed, 04 Apr 2007 09:10:45 +0200 > From: Glenn Lawyer <d.g.lawyer(a)medisin.uio.no> > Subject: [Freesurfer] Freesurfer and R > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <46134F75.2070803(a)medisin.uio.no> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I'm also using R to look at some FreeSurfer data, mostly to play with > significance values. To do this, I convert them to ascii (mris_convert) > and load them into R with the read.table function. When I am done, I > write a new ascii file, mris_convert it back to a *.w or *.sig, and load > it into tksurfer. The function to write the file is trivial, but here it > is for completeness: > > ## more FreeSurfer specific stuff. > ## the modified significance values in a text file called "fdr.txt" > ## posindex is a global variable tracking which pvalues were > ## positive in the original sig file > ## (recall that FS stores sig values as log10(sig), with the > ## sign indicating direction of effect) > ## vindex is a global variable tracking the vertex number > ## associated with a given sig value > write.fs.output <- function(){ > fdr <- dget('fdr.txt') > fdr <- log10(fdr) > fdr[posindex] <- fdr[posindex] * -1 > cat("0.000\n", length(fdr), "\n", file="AA-TT_cmfdr.ascii") > for (i in 1:length(fdr)){ > cat(vindex[i], fdr[i], "\n", sep="\t", > file="AA-TT_fdr.ascii", append=TRUE) > } > } >

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Recommended Linux flavour
by Alex Wade 05 Apr '07

05 Apr '07

We are about to install a few Linux workstations, primarily to run Freesurfer and MNISuite. Can I check on what the best Linux flavour is? Do you still recommend CentOS 4? thanks Alex -- A.R. Wade Ph.D. Associate Scientist The Smith-Kettlewell Eye Research Institute 2318 Fillmore Street San Francisco, CA 94115 tel. 415 345 2083 fax. 309 416 6533

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erroneous 'no space left on device' error
by Kathryn Devaney 04 Apr '07

04 Apr '07

Hi all, I am trying to run an analysis in /space/stego/2/ (on machine 'whatever') and I can run mkanalysis, but when I try to run selxavg, I get the following error, in both std and dev environments: whatever:subj27/mystudy% selxavg-sess -sf sessid -df sesspar -analysis m4_fmc -noomnibus INFO: WhitenFlag = 0 -------------------------------------------------------------- selxavg-sess logfile is /autofs/space/stego_002/users/kdevaney/m4/subj27/mystudy/log/selxavg-sess-bold-m4_fmc-070404224944.log -------------------------------------------------------------- ------------------------------------------- /autofs/space/stego_002/users/kdevaney/m4/subj27 Wed Apr 4 22:49:45 EDT 2007 INFO (subj27): RunList = 003 004 005 007 008 009 010 011 012 013 014 015 cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cp: writing `/tmp/par.11619': No space left on device cat: /tmp/countncond.11619: No such file or directory however: whatever:subj27/mystudy% df . -h Filesystem Size Used Avail Use% Mounted on bronto:/local_mount/space/stego/2 63G 5.7G 57G 10% /autofs/space/stego_002 There is clearly plenty of space left. Any help is appreciated, thanks! Katie

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Matching slice location in dicoms to the .mgz format
by Trina Kok 04 Apr '07

04 Apr '07

Hi all, I have a question on matching slice location between dicoms and the freesurfer output. I have a set of 120 dicom files and I ran it through the autorecon process in freesurfer. From the viewer with tkmedit, there are 180 files (slice 218 to 39 in trans view) that corresponded to scanning, i.e. with some image scanned. I think the rest of the 256 slices are interpolations, but how does the 180 slices map to the 120 dicom files? I'm asking because I am trying to map a dicom file with a specific slice location to the .mgz images. Thank you. Regards, Trina

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Freesurfer and R
by Glenn Lawyer 04 Apr '07

04 Apr '07

Hi, I'm also using R to look at some FreeSurfer data, mostly to play with significance values. To do this, I convert them to ascii (mris_convert) and load them into R with the read.table function. When I am done, I write a new ascii file, mris_convert it back to a *.w or *.sig, and load it into tksurfer. The function to write the file is trivial, but here it is for completeness: ## more FreeSurfer specific stuff. ## the modified significance values in a text file called "fdr.txt" ## posindex is a global variable tracking which pvalues were ## positive in the original sig file ## (recall that FS stores sig values as log10(sig), with the ## sign indicating direction of effect) ## vindex is a global variable tracking the vertex number ## associated with a given sig value write.fs.output <- function(){ fdr <- dget('fdr.txt') fdr <- log10(fdr) fdr[posindex] <- fdr[posindex] * -1 cat("0.000\n", length(fdr), "\n", file="AA-TT_cmfdr.ascii") for (i in 1:length(fdr)){ cat(vindex[i], fdr[i], "\n", sep="\t", file="AA-TT_fdr.ascii", append=TRUE) } } -- -------------------------------------- I'm only in it for the glory . + Glenn Lawyer + + +352 661 967 244 + + Instituttgruppe for psykiatri + + Seksjon Vinderen + + PB 85 Vinderen + + 0319 Oslo + + http://folk.uio.no/davidgl + +++++++++++++++++++++++++++++++++++:)

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segmentation fault during autorecon 2
by Mithra 03 Apr '07

03 Apr '07

Hello FS Group, I get "segmentation fault" error during autorecon2 step. I checked the talairach transformation. It seemed to be fine. The skull strip did not seem to be correct. I manually edited the brainmask.mgz and saved the data. But still I get the error. I am not sure what the problem is. Any help would be great! I have the output form mri_info for the original surface. . Thanks. Mithra. Output for mri_info: mri_info $SUBJECTS_DIR/asm1_004/mri/orig.mgz Volume information for /usr/pubsw/freesurfer/subjects/asm1_004/mri/orig.mgz type: MGH dimensions: 301 x 301 x 301 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 301.000 xstart: -150.5, xend: 150.5 ystart: -150.5, yend: 150.5 zstart: -150.5, zend: 150.5 TR: 4.97 msec, TE: 1.21 msec, TI: 500.00 msec, flip angle: 11.00 deg rees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 40.3653 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -26.5037 talairach xfm : /usr/pubsw/freesurfer/subjects/asm1_004/mri/transforms/talairach .xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 150.5000 0.0000 0.0000 1.0000 -110.1347 0.0000 -1.0000 0.0000 123.9963 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 150.5000 -0.0000 -0.0000 -1.0000 123.9963 0.0000 1.0000 0.0000 110.1347 0.0000 0.0000 0.0000 1.0000

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Freesurfer April 2007